Darths & Droids has Chancellor Valorum as such an over-the-top Evil Chancellor that he yells "Kneel before Valorum!", as a reference to Zod from the Superman film. Both Chancellor Valorum and Zod were played by Terence Stamp, whom the authors felt "deserved some slightly more memorable lines." The "GM plans" also had Valorum originally named as "Zod".
In a Concerned strip, Dr. Breen is seen reading a news paper and mentioning there is an I Spy marathon running that night. In Half-Life 2, Dr. Breen was voiced by Robert Culp, who played Kelly Robinson in I Spy.
In the Irregular Webcomic! "Espionage" theme, during the From Russia with Love parody, James Stud comments to Kerim Bey that he'll never see either of the wrestling gypsy women again, and Bey replies "I'm Nassau sure about that". In the film, one of the women was played by Martine Beswick, who later played Paula Caplan in the Nassau scenes of Thunderball.
ThisCelestia's Servant Interview comic interviews Cheese Sandwich, so of course there are several references to "Weird Al" Yankovic songs.
Canadian Flash master Ian Kirby of Broken Saints fame makes a cameo on the DVD voice tracks as a Canadian soldier.
One KateModern video posted by Gavin is entitled "Half the Week Away", a reference to Oasis' "Half the World Away", the Theme Song to The Royle Family. Gavin is played by Ralf Little, who played Antony in The Royle Family.
In the musical episode of Legend of Neil, a Zelda parody, she plays the Fairy, stating rather casually that she's "not really into online musicals", referencing her role in Dr. Horrible. She, of course, makes this statement just before bursting into song.
This entry borders between this and a bout of comedic prophesy: in LittleKuriboh's flagship work, an episode shows Tristan coming up on a motorcycle, and when he's asked about it, he replies: 'In the Future, card games will be played on motorbikes.' Fast Forward to the Dub release of Yu-Gi-Oh! 5Ds, and we see Frank Frankson, Tristan's voice actor cast as the lead character of said show, Yusei Fudo.
In one Two Best Friends Play video, when Matt and Pat are playing Captain America: Super Soldier they come across a picture of pre-Red Skull Hugo Weaving. They take turns wondering why Elrond, Agent Smith, Megatron, and V would have portraits in a German castle before running out of Hugo Weaving movies they can remember.